Elisa Peripolli

• PhD Student at São Paulo State University

Background Selecting animals for feed efficiency directly impacts the profitability of the beef cattle industry, which contributes to minimizing the environmental footprint of beef production. Genetic and environmental factors influence animal feed efficiency, leading to phenotypic variability when exposed to different environmental conditions (i.e...

Context In beef cattle populations, there is little evidence regarding the minimum number of genetic markers needed to obtain reliable genomic prediction and imputed genotypes. Aims This study aimed to evaluate the impact of single nucleotide polymorphism (SNP) marker density and minor allele frequency (MAF), on genomic predictions and imputation...

This study aimed to assess the impact of differential weighting in genomic regions harboring candidate causal loci on the genomic prediction accuracy and dispersion for growth and carcass‐related traits in Nelore cattle. The dataset contained 168 793 phenotypic records for adjusted weight at 450 days of age (W450), 83 624 for rib eye area (REA), 24...

The aim of this work was to evaluate the impact of applying genomic information in pedigree uncertainty situations on genetic evaluations for growth- and cow productivity–related traits in Nelore commercial herds. Records for accumulated cow productivity (ACP) and adjusted weight at 450 days of age (W450) were used, as well as genotypes of register...

Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome‐wide assessment of copy number variations (CNVs) based on whole‐genome re‐sequencing data was...

The objective of this study was to obtain (co)variance components, heritability, and genetic and phenotypic correlation estimates for feed efficiency and feed behaviour‐related indicator traits. Further, it aimed to predict the direct and correlated responses for feed efficiency traits when selection was applied for feeding behaviour‐related traits...

Background Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in...

This study aimed to estimate prediction ability and genetic parameters for residual feed intake (RFI) calculated using a regression equation for each test (RFItest) and for the whole population (RFIpop) in Nellore beef cattle. It also aimed to evaluate the correlations between RFIpop and RFItest with growth, reproductive, and carcass traits. Genoty...

In Nellore beef cattle, studies addressing genetic correlations between ultrasound marbling content and other economically important traits are still incipient. Therefore, this work aimed to estimate heritability and genetic correlations between ultrasound marbling content in the longissimus dorsi muscle (MARB) and growth, reproductive, feed effici...

This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High‐Density Bovine BeadChip. In or...

Context A frame score prediction equation developed specifically for Nellore cattle could be an auxiliary tool to improve mating decisions on the basis of feed resources and production-system objectives. Aims Estimate genetic parameters for frame by using a prediction equation developed for Nellore cattle and genetic associations between frame sco...

Bos indicus cattle acquired very particular traits to thrive in distinct environments based on the evolutionary adaptation process they have undergone, becoming particularly relevant for tropical production systems. In this review we present and discuss the current status of the application of genomic selection (GS) for Bos indicus (Nellore) breed,...

Beef is a source of essential fatty acids (EFA), linoleic (LA) and alpha-linolenic (ALA) acids, which protect against inflammatory and cardiovascular diseases in humans. However, the intramuscular EFA profile in cattle is a complex and polygenic trait. Thus, this study aimed to identify potential regulatory genes of the essential fatty acid profile...

The beef fatty acid (FA) profile has the potential to impact human health, and displays polygenic and complex features. This study aimed to identify the transcriptomic FA profile in the longissimus thoracis muscle in Nellore beef cattle finished in feedlot. Forty‐four young bulls were sampled to assess the beef FA profile by considering 14 phenotyp...

This study aimed to estimate genetic parameters and the prediction ability and bias of the genomic values for residual feed intake (RFI) using genotypic and phenotypic records from 8,354 Nellore animals. The RFI was calculated using a regression equation for each test (RFI test ) and for the whole population (RFI pop ). An analysis of variance (ANO...

This study aimed to investigate the prediction ability for growth and maternal traits using different low-density customized SNP arrays selected by informativeness and distribution of markers across the genome employing single-step genomic BLUP (ssGBLUP). Phenotypic records for adjusted weight at 210 and 450 days of age were utilized. A total of 94...

We evaluated a novel frame score system for Nellore cattle raised on pasture (Guimarães et al., 2020 J, Anim. Sci. 98 (Suppl. 4)). Growth traits included age-adjusted weights (kg) at birth (W0), 120 (W120), 210 (W210) and 450 (W450) days of age, and adult weight (AW). Carcass traits (by ultrasound) included ribeye area (REA, cm2), 12th-13th rib bac...

Frame score systems developed for Bos taurus breeds do not translate well for Bos indicus breeds, as these tend to be taller. We evaluated a novel frame score system for Nellore cattle raised on pasture [Guimaraes et al., 2020 J, Anim. Sci. 98 (Suppl. 4)]. Traits included adjusted scrotal circumference (cm) at 365 (SC365) and 450 (SC450) days of ag...

The multiple sire system (MSS) is a common mating scheme in extensive beef production systems. However, MSS does not allow paternity identification and lead to inaccurate genetic predictions. The objective of this study was to investigate the implementation of single-step genomic BLUP (ssGBLUP) in different scenarios of uncertain paternity in the e...

This study aimed to identify structural variations in the form of runs of homozygosity (ROH) and copy number variants (CNVs) in the genome of the Brazilian Senepol cattle and to better explore the potential biological functions of the genes located within such regions. A total of 140 animals were genotyped with the GeneSeek® Genomic Profiler™ Bovin...

Gene–gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene–gene interactions using the empirical Hilbert–Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile...

The reduction of age at puberty in young bulls is an important issue to reduce the growing phase and promote substantial savings in production cost as well as to reduce the generation interval. This study aims to estimate genetic parameters for age at puberty in males (APM), growth, carcass, and reproductive-related traits in young Nelore bulls. Ad...

Background: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted...

The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The int...

The aim of this study was to evaluate the genomic predictions using the single‐step genomic best linear unbiased predictor (ssGBLUP) method based on SNPs and haplotype markers associated with beef fatty acids (FAs) profile in Nelore cattle. The data set contained records from 963 Nelore bulls finished in feedlot (±90 days) and slaughtered with appr...

The objective of this study was to evaluate the effect of nutritional management during rearing and finishing phases on beef fatty acid composition, and carcass and beef quality traits of Hereford cattle. The study used 240 castrated male calves weaned at 8 months of age, and with an average weight of 170 ± 17 kg. After weaning, the experiment was...

The aim of this study was to assess the distribution of runs of homozygosity (ROH) and autozygosity islands in the composite Montana Tropical® beef cattle to explore hotspot regions which could better characterize the different biological types within the composite breed. Montana animals (n = 1,436) were genotyped with the GGP‐LD BeadChip (~30,000...

This study was conducted to characterize metabolic differences between high feed efficiency (HFE) and low feed efficiency (LFE) chickens to investigate why feed efficient chickens are more susceptible to muscle abnormalities such as wooden breast disease. Gene expression profiles were generated by RNA sequencing of pectoralis major muscle samples f...

The aim of this study was to estimate genetic parameters for different precocious calving criteria and their relationship with reproductive, growth, carcass and feed efficiency in Nellore cattle using the single‐step genomic BLUP. The reproductive traits used were probability of precocious calving (PPC) at 24 (PPC24), 26 (PPC26), 28 (PPC28) and 30...

The aim of the present study was to compare the predictive ability of SNP-BLUP model using different pseudo-phenotypes such as phenotype adjusted for fixed effects, estimated breeding value, and genomic estimated breeding value, using simulated and real data for beef FA profile of Nelore cattle finished in feedlot. A pedigree with phenotypes and ge...

Background: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigr...

The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with maternal related traits in Santa Inês sheep breed adapted to tropical climate. Phenotypic records for maternal efficiency (ME), metabolic maternal efficiency (MME), twin lambing (TL), adult weight (AW), metabolic adult weight (MAW)...

This study was carried out to estimate the heritability and genetic correlations between adjusted weights at 210 (W210) and 450 (W450) days of age, scrotal circumference adjusted at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), probability of precocious calving (PPC), stayability (STAY), ribeye area (REA), subcutaneous backfa...

The causal mutation for polledness in Nelore (Bos taurus indicus) breed seems to have appeared first in Brazil in 1957. The expression of the polled trait is known to be ruled by a few groups of alleles in taurine breeds; however, the genetic basis of this trait in indicine cattle is still unclear. The aim of this study was to identify genomic regi...

Improving reproductive indexes is of extreme importance in beef cattle production systems, as well as investigating new methodologies and traits in order to increase genetic gains for reproduction. Reproductive efficiency directly affects the profitability and productivity of herds, being an important criterion in breeding programs. The objective o...

The aim of this study was to analyze the association between the copy number variation regions (CNVRs) and fatty acid profile phenotypes for saturated (SFA), monosaturated (MUFA), polyunsaturated (PUFA), ω6 and ω3 fatty acids, PUFA/SFA and ω6/ω3 ratios, as well as for their sums, in Nellore cattle (Bos primigenius indicus). A total of 963 males wer...

The aim of this study was to analyze the association between copy number variations regions (CNVRs) and saturated fatty acid (SFA) profile phenotypes in the Longissimus thoracis muscle of Nellore cattle finished in feedlot. A total of 963 Nellore bulls with phenotype for SFA profiles were genotyped using the Illumina BovineHD BeadChip (Illumina, Sa...

Background: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dair...

The occurrence of polled Nelore has only been reported in Brazil. The expression of the polled trait is known to be ruled by a few group of alleles in taurine breeds; however, the genetic basis of this traits in indicine cattle is still not clear. In this study, we aimed to identify genomic regions associated with the hornless trait in Nelore. A to...

Background: The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly Haemonchus contortus, in a breed of sheep adapted to tropical climate. Phenotypes evaluations were performed to verify resistance to gastrointestinal parasites, an...

The aim of the present study was to analyze the distribution of CNV regions (CNVRs) as well as to address hypothesis about the natural/artificial selection process in Nellore cattle. A total of 399,361 CNVs were identified, using the PennCNV algorithm, in 3,794 Nellore cattle (Bos taurus indicus) genotyped with the Bovine HD BeadChip array. The def...

The objective of this study was to investigate the application of BLUP and single step genomic BLUP (ssGBLUP) models in different scenarios of paternity uncertainty with different strategies of scaling the G matrix to match the A22 matrix, using simulated data for beef cattle. Genotypes, pedigree, and phenotypes for age at first calving (AFC) and w...

Data edition, variance components estimation, breeding value accuracies of all analyses. (RAR)

The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly Haemonchus contortus, in Santa Inês sheep, a Brazilian breed adapted to tropical climate. The degree of anemia assessed by the FAMACHA card (FAM) and the egg counts per gram of...

This study was carried out to identify genomic regions associated with beef tenderness (Warner-Bratzler shear force, WBSF) and to evaluate the prediction ability using preselected markers based on the genome-wide association study (GWAS) results in an experimental Nelore cattle population. The dataset was provided by Guaporé Agropecuária S/A – OB R...

The aim of this study was to identify genomic regions associated with the total amount of saturated (SFA), monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids in the beef of Nellore cattle. The investigated dataset contained records from 963 Nellore bulls, about two years old, finished in feedlot (90 days). Meat samples of Longissimus do...

Different nutritional management during the rearing and finishing periods can determine changes on beef fatty acid profile. Beef lipid composition was quantified in 224 male Hereford calves weaned at 8 wk of age with an average initial live weight (LW) of 170 ± 17 kg. After weaning, 4 nutritional treatments were imposed to obtain different daily LW...

The objective of this study was to investigate the application of BLUP and ssGBLUP in different scenarios of uncertain paternity using data from a Nellore cattle population. The analyzed data set was provided by the National Association of Farmers and Researchers (ANCP). The data set contained information from 18 Nellore herds located in the southe...

The objective of the present study was to evaluate the effect of nutritional management treatments during the rearing period on the performance and carcass traits of Hereford steers finished either on pasture or in feedlot. Two hundred and forty male Hereford calves, weaned at 8 months of age with an average weight of 170 ± 17 kg, were used. After...

The objective of this study was to compare SNP-BLUP, BayesCπ, BayesC and Bayesian Lasso methodologies to predict the direct genomic value for saturated, monounsaturated, and polyunsaturated fatty acid profile, omega 3 and 6 in the Longissimus thoracis muscle of Nellore cattle finished in feedlot. A total of 963 Nellore bulls with phenotype for fatt...

Runs of homozygosity (ROH) patterns are not seen to be randomly distributed across the genome and genomic regions sharing ROH potentially contain genes associated with genetic improvement in livestock. The aim of this study was to identify ROH shared by more than 50% of the samples so as to prospect dairy-related genes inside those ROH islands. Gir...

Background Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. Re...

The aim of the present study was to estimate covariance components and genetic parameters for beef fatty acid (FA) composition of intramuscular fat in the longissimus thoracis muscle in Nelore bulls finished in feedlot. Twenty-two FAs were selected. The heritability estimates for individual FAs ranged from 0.01 to 0.35. The heritability estimates f...

This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight...

The objective of this study was to estimate the genetic–quantitative relationships between the beef fatty acid profile with the carcass and meat traits of Nellore cattle. A total of 1826 bulls finished in feedlot conditions and slaughtered at 24 months of age on average were used. The following carcass and meat traits were analysed: subcutaneous fa...

Foi desenvolvido o modelo bioeconômico nominado de Beef Management System para a obtenção de valores econômicos em quatro sistemas de recria e engorda de bovinos. Dos modelos analisados, dois utilizaram machos inteiros da raça Nelore e os outros dois machos inteiros cruzados (½ sangue taurino; ½ sangue zebu). Para cada grupamento genético estipulou...

A bio-economic model called Beef Management System was developed to obtain economic values for four growth and finishing cattle production system. A total of four rearing and finishing systems, two were composed by Nellore cattle and the others by crossbred cattle (½ Taurine; ½ Zebu) were tested. For each genetic group, two production systems were...